pbreheny/deepn

Dynamic enrichment for evaluation of protein networks

Dynamic Enrichment for Evaluation of Protein Networks

This is the accompanying R package for the DEEPN project.

Installation

deepn has several package dependencies, most notably JAGS and Bioconductor. JAGS must be setup outside R (see link for instructions), while Bioconductor can be installed within R via:

source("https://bioconductor.org/biocLite.R")
biocLite()

Once that is done, you can install deepn via remotes (which itself can be installed via install.packages("remotes")):

remotes::install_github("pbreheny/deepn")

Basic usage

Once installed, deepn can be used to analyze the output from deepn with

require(deepn)
analyzeDeepn("deepn.config")

where "deepn.config" is the name of the configuration file that DEEPN outputs containing path names to all the .csv files needed in the analysis. This will create a file, stat.csv, containing a table of summary statistics for each gene.

The above analysis may take a while to run, depending on the threshold. To run a "quick" version of the analysis, you can use

analyzeDeepn("deepn.config", debug=TRUE)

which applies a very high PPM threshold of 200 prior to analysis, so that it should only take a minute or two to complete.